Abies nordmanniana is a major Christmas tree species in Europe, but their uneven and prolonged growth slows down their production. By a 16S and 18S rRNA gene amplicon sequencing approach, we performed a characterization of root-associated bacterial and fungal communities for three-year-old A. nordmanniana plants collected from two nurseries in Denmark and Germany and displaying different growth patterns (small versus tall plants). Proteobacteria had the highest relative abundance at both sampling sites and plant sizes, and Ascomycota was the most abundant fungal phylum. At the order level, Acidobacteriales, Actinomycetales, Burkholderiales, Rhizobiales, and Xanthomonadales represented the bacterial core microbiome of A. nordmanniana, independently of the sampling site or plant size, while the fungal core microbiome included members of the Agaricales, Hypocreales, and Pezizales. Principal Coordinate Analysis indicated that both bacterial and fungal communities clustered according to the sampling site pointing to the significance of soil characteristics and climatic conditions for the composition of root-associated microbial communities. Major differences between communities from tall and small plants were a dominance of the potential pathogen Fusarium (Hypocreales) in the small plants from Germany, while Agaricales, that includes reported beneficial ectomycorrhizal fungi, dominated in the tall plants. An evaluation of plant root antioxidative enzyme profiles showed higher levels of the antioxidative enzymes ascorbate peroxidase, peroxidase, and superoxide dismutase in small plants compared to tall plants. We suggest that the higher antioxidative enzyme activities combined with the growth arrest phenotype indicate higher oxidative stress levels in the small plants. Additionally, the correlations between the relative abundances of specific taxa of the microbiome with the plant antioxidative enzyme profiles were established. The main result was that many more bacterial taxa correlated positively than negatively with one or more antioxidative enzyme activity. This may suggest that the ability of bacteria to increase plant antioxidative enzyme defenses is widespread.